Variant report

Variant	rs272498
Chromosome Location	chr1:86818846-86818847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86817766..86820014-chr1:86820204..86822305,3	K562	blood:
2	chr1:86817633..86819266-chr1:86820612..86822159,2	K562	blood:

Variant related genes	Relation type
ENSG00000122417	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10493789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10747328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873782	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs1158505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1182102	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1334143	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1334145	0.95[CEU][hapmap];0.87[YRI][hapmap]
rs1334146	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1334147	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1334148	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1334150	0.86[CHB][hapmap]
rs166626	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166627	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129078	0.86[ASN][1000 genomes]
rs175363	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185655	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap]
rs187971	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1931363	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2104962	0.83[AFR][1000 genomes]
rs2104963	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2151708	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151709	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250857	0.93[CHB][hapmap]
rs272491	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272492	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272494	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272510	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272511	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272516	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs405424	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs410807	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4288573	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs450927	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs452865	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs567133	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs569912	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61804060	0.86[ASN][1000 genomes]
rs6695671	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7527383	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs883200	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1792405	chr1:86814270-86825639	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86806400-86823600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:86810400-86819200	Weak transcription	NHLF	lung
4	chr1:86810600-86819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:86810800-86819400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:86811200-86819000	Weak transcription	Fetal Lung	lung
7	chr1:86811600-86819000	Weak transcription	Brain Angular Gyrus	brain
8	chr1:86812000-86819200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:86813000-86819200	Weak transcription	Left Ventricle	heart
10	chr1:86813200-86819200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:86813600-86819400	Weak transcription	Osteobl	bone
12	chr1:86813800-86836400	Weak transcription	Lung	lung
13	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
14	chr1:86815000-86819000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:86815200-86819000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
17	chr1:86815600-86819400	Weak transcription	Aorta	Aorta
18	chr1:86816000-86819200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:86816000-86819400	Weak transcription	Brain Germinal Matrix	brain
20	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:86816200-86819200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:86816200-86824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:86816200-86826200	Weak transcription	A549	lung
24	chr1:86816400-86819000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:86816400-86820400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:86816600-86819000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:86816800-86819200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:86817000-86819200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:86817200-86819200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:86817200-86820400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:86817200-86820400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
33	chr1:86817400-86819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:86817400-86819000	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:86817400-86819000	Weak transcription	NHEK	skin
36	chr1:86817400-86819200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:86817400-86819200	Weak transcription	Spleen	Spleen
38	chr1:86817400-86819200	Weak transcription	HSMMtube	muscle
39	chr1:86817400-86820600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:86817400-86820800	Strong transcription	Dnd41	blood
41	chr1:86817400-86821000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:86817400-86824400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:86817400-86824400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:86817400-86826000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:86817400-86826000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:86817400-86826200	Strong transcription	HUVEC	blood vessel
47	chr1:86817600-86819200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:86817600-86819200	Weak transcription	Brain Anterior Caudate	brain
49	chr1:86817600-86819200	Weak transcription	Brain Substantia Nigra	brain
50	chr1:86817600-86819200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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